From c0be7bbdf90fe9b2a944b947cf0cc2006ba949ba Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 19 Jan 2026 20:48:15 +0000 Subject: [PATCH 1/3] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.14.11 → v0.14.13](https://github.com/astral-sh/ruff-pre-commit/compare/v0.14.11...v0.14.13) - https://github.com/adrienverge/yamllint/: v1.37.1 → v1.38.0 --- .pre-commit-config.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index bca33d7..20a01e4 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -17,7 +17,7 @@ repos: - id: trailing-whitespace exclude: "tests/cis_tests/.*" - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.14.11 + rev: v0.14.13 hooks: - id: ruff-check args: [--fix, --exit-non-zero-on-fix] @@ -34,7 +34,7 @@ repos: hooks: - id: gitleaks - repo: https://github.com/adrienverge/yamllint/ - rev: v1.37.1 + rev: v1.38.0 hooks: - id: yamllint - repo: https://github.com/ComPWA/taplo-pre-commit From e828ecbbea7b11cfb244d5d08b657a9d2a01e9ce Mon Sep 17 00:00:00 2001 From: Chen Zhang Date: Mon, 19 Jan 2026 17:21:41 -0500 Subject: [PATCH 2/3] fix(deps): update dependencies to resolve security vulnerabilities - urllib3 >= 2.6.3 (CVE-2026-21441) - filelock >= 3.20.3 (CVE-2026-22701) - virtualenv >= 20.36.1 (CVE-2026-22702) - Remove --ignore-vuln flag from audit-deps task since urllib3 fix is now available Co-Authored-By: Claude Opus 4.5 --- pixi.lock | 60 +++++++++++++++++++++++++------------------------- pyproject.toml | 7 +++--- 2 files changed, 34 insertions(+), 33 deletions(-) diff --git a/pixi.lock b/pixi.lock index 4e68de5..497ee73 100644 --- a/pixi.lock +++ b/pixi.lock @@ -54,7 +54,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/noarch/editables-0.5-pyhd8ed1ab_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/exceptiongroup-1.3.1-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/execnet-2.1.2-pyhd8ed1ab_0.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.20.1-pyhd8ed1ab_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.20.3-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2 @@ -273,11 +273,11 @@ environments: - conda: https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.15.0-pyhcf101f3_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/tzdata-2025c-hc9c84f9_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/ukkonen-1.0.1-py314h9891dd4_6.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.6.2-pyhd8ed1ab_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.6.3-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/userpath-1.9.2-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/uv-0.9.21-h76e24b7_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/versioningit-3.3.0-pyhd8ed1ab_0.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/virtualenv-20.35.4-pyhd8ed1ab_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/virtualenv-20.36.1-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/webencodings-0.5.1-pyhd8ed1ab_3.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/xcb-util-0.4.1-h4f16b4b_2.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/xcb-util-image-0.4.0-hb711507_2.conda @@ -360,7 +360,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/noarch/editables-0.5-pyhd8ed1ab_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/exceptiongroup-1.3.1-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/execnet-2.1.2-pyhd8ed1ab_0.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.20.1-pyhd8ed1ab_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.20.3-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/osx-arm64/giflib-5.2.2-h93a5062_0.conda - conda: https://conda.anaconda.org/conda-forge/osx-arm64/glib-2.86.3-h7ee6e74_0.conda - conda: https://conda.anaconda.org/conda-forge/osx-arm64/glib-tools-2.86.3-hb9d6e3a_0.conda @@ -546,11 +546,11 @@ environments: - conda: https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.15.0-pyhcf101f3_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/tzdata-2025c-hc9c84f9_1.conda - conda: https://conda.anaconda.org/conda-forge/osx-arm64/ukkonen-1.0.1-py314h6b18a25_6.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.6.2-pyhd8ed1ab_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.6.3-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/userpath-1.9.2-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/osx-arm64/uv-0.9.21-hab132b7_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/versioningit-3.3.0-pyhd8ed1ab_0.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/virtualenv-20.35.4-pyhd8ed1ab_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/virtualenv-20.36.1-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/webencodings-0.5.1-pyhd8ed1ab_3.conda - conda: https://conda.anaconda.org/conda-forge/osx-arm64/xorg-libxau-1.0.12-hc919400_1.conda - conda: https://conda.anaconda.org/conda-forge/osx-arm64/xorg-libxdmcp-1.1.5-hc919400_1.conda @@ -629,7 +629,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/noarch/distlib-0.4.0-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/exceptiongroup-1.3.1-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/executing-2.2.1-pyhd8ed1ab_0.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.20.1-pyhd8ed1ab_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.20.3-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2 @@ -850,9 +850,9 @@ environments: - conda: https://conda.anaconda.org/conda-forge/linux-64/ukkonen-1.0.1-py314h9891dd4_6.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/unicodedata2-17.0.0-py314h5bd0f2a_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/uri-template-1.3.0-pyhd8ed1ab_1.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.6.2-pyhd8ed1ab_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.6.3-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/versioningit-3.3.0-pyhd8ed1ab_0.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/virtualenv-20.35.4-pyhd8ed1ab_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/virtualenv-20.36.1-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/wcwidth-0.2.14-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/webcolors-25.10.0-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/webencodings-0.5.1-pyhd8ed1ab_3.conda @@ -942,7 +942,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/noarch/distlib-0.4.0-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/exceptiongroup-1.3.1-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/executing-2.2.1-pyhd8ed1ab_0.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.20.1-pyhd8ed1ab_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.20.3-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/fonttools-4.61.1-pyh7db6752_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/fqdn-1.5.1-pyhd8ed1ab_1.conda - conda: https://conda.anaconda.org/conda-forge/osx-arm64/freetype-2.14.1-hce30654_0.conda @@ -1135,9 +1135,9 @@ environments: - conda: https://conda.anaconda.org/conda-forge/osx-arm64/ukkonen-1.0.1-py314h6b18a25_6.conda - conda: https://conda.anaconda.org/conda-forge/osx-arm64/unicodedata2-17.0.0-py314h0612a62_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/uri-template-1.3.0-pyhd8ed1ab_1.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.6.2-pyhd8ed1ab_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.6.3-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/versioningit-3.3.0-pyhd8ed1ab_0.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/virtualenv-20.35.4-pyhd8ed1ab_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/virtualenv-20.36.1-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/wcwidth-0.2.14-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/webcolors-25.10.0-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/webencodings-0.5.1-pyhd8ed1ab_3.conda @@ -2012,8 +2012,8 @@ packages: timestamp: 1733208220327 - pypi: ./ name: examplepyapp - version: 0.2.0.dev294 - sha256: 414acc4f7dbd40d7f21f6a4df931de53b7e6dc11889dd046ceb944c478aea7e8 + version: 0.2.0.dev296 + sha256: 7531cb9d7ca7263b4a84115bd142e6136265ed19daf0fd1da9b28ec9165939a6 requires_dist: - bm3d-streak-removal>=0.2.0,<0.3 - numpy>=2.2,<3 @@ -2053,14 +2053,14 @@ packages: license_family: MIT size: 30753 timestamp: 1756729456476 -- conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.20.1-pyhd8ed1ab_0.conda - sha256: 8028582d956ab76424f6845fa1bdf5cb3e629477dd44157ca30d45e06d8a9c7c - md5: 81a651287d3000eb12f0860ade0a1b41 +- conda: https://conda.anaconda.org/conda-forge/noarch/filelock-3.20.3-pyhd8ed1ab_0.conda + sha256: 8b90dc21f00167a7e58abb5141a140bdb31a7c5734fe1361b5f98f4a4183fd32 + md5: 2cfaaccf085c133a477f0a7a8657afe9 depends: - python >=3.10 license: Unlicense - size: 18609 - timestamp: 1765846639623 + size: 18661 + timestamp: 1768022315929 - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2 sha256: 58d7f40d2940dd0a8aa28651239adbf5613254df0f75789919c4e6762054403b md5: 0c96522c6bdaed4b1566d11387caaf45 @@ -6798,9 +6798,9 @@ packages: license_family: MIT size: 23990 timestamp: 1733323714454 -- conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.6.2-pyhd8ed1ab_0.conda - sha256: f4302a80ee9b76279ad061df05003abc2a29cc89751ffab2fd2919b43455dac0 - md5: 4949ca7b83065cfe94ebe320aece8c72 +- conda: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.6.3-pyhd8ed1ab_0.conda + sha256: af641ca7ab0c64525a96fd9ad3081b0f5bcf5d1cbb091afb3f6ed5a9eee6111a + md5: 9272daa869e03efe68833e3dc7a02130 depends: - backports.zstd >=1.0.0 - brotli-python >=1.2.0 @@ -6809,8 +6809,8 @@ packages: - python >=3.10 license: MIT license_family: MIT - size: 102842 - timestamp: 1765719817255 + size: 103172 + timestamp: 1767817860341 - conda: https://conda.anaconda.org/conda-forge/noarch/userpath-1.9.2-pyhd8ed1ab_0.conda sha256: 26e53b42f7fa1127e6115a35b91c20e15f75984648b88f115136f27715d4a440 md5: 946e3571aaa55e0870fec0dea13de3bf @@ -6856,19 +6856,19 @@ packages: license_family: MIT size: 167034 timestamp: 1751113901223 -- conda: https://conda.anaconda.org/conda-forge/noarch/virtualenv-20.35.4-pyhd8ed1ab_0.conda - sha256: 77193c99c6626c58446168d3700f9643d8c0dab1f6deb6b9dd039e6872781bfb - md5: cfccfd4e8d9de82ed75c8e2c91cab375 +- conda: https://conda.anaconda.org/conda-forge/noarch/virtualenv-20.36.1-pyhd8ed1ab_0.conda + sha256: fa0a21fdcd0a8e6cf64cc8cd349ed6ceb373f09854fd3c4365f0bc4586dccf9a + md5: 6b0259cea8ffa6b66b35bae0ca01c447 depends: - distlib >=0.3.7,<1 - - filelock >=3.12.2,<4 + - filelock >=3.20.1,<4 - platformdirs >=3.9.1,<5 - python >=3.10 - typing_extensions >=4.13.2 license: MIT license_family: MIT - size: 4401341 - timestamp: 1761726489722 + size: 4404318 + timestamp: 1768069793682 - conda: https://conda.anaconda.org/conda-forge/noarch/wcwidth-0.2.14-pyhd8ed1ab_0.conda sha256: e311b64e46c6739e2a35ab8582c20fa30eb608da130625ed379f4467219d4813 md5: 7e1e5ff31239f9cd5855714df8a3783d diff --git a/pyproject.toml b/pyproject.toml index b8c3002..2b72c35 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -110,8 +110,9 @@ pyqt = "*" # pip-audit h2 = ">=4.3.0" # Known vulnerability in <4.3.0 brotli = ">=1.2.0" -urllib3 = ">=2.6.0" # Known vulnerability in <2.6.0 -filelock = ">=3.20.1" # Known vulnerability in <3.20.1 +urllib3 = ">=2.6.3" # Known vulnerability in <2.6.3 +filelock = ">=3.20.3" # Known vulnerability in <3.20.3 +virtualenv = ">=20.36.1" # Known vulnerability in <20.36.1 [tool.pixi.pypi-dependencies] # PyPI dependencies, including this package to allow local editable installs @@ -211,7 +212,7 @@ conda-publish = { cmd = "anaconda upload *.conda", description = "Publish the .c ] } # Misc # urllib3 is only used for package and deployment -audit-deps = { cmd = "pip-audit --local -s osv --ignore-vuln CVE-2026-21441", description = "Audit the package dependencies for vulnerabilities" } +audit-deps = { cmd = "pip-audit --local -s osv", description = "Audit the package dependencies for vulnerabilities" } # Cleaning clean = { cmd = 'rm -rf .pytest_cache .ruff_cache **/*.egg-info **/dist **/__pycache__', description = "Clean up various caches and build artifacts" } clean-conda = { cmd = "rm -f *.conda", description = "Clean the local .conda build artifacts" } From 6252b036d4f5e6152f3ca62d8a97d650f9502c42 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 19 Jan 2026 22:22:07 +0000 Subject: [PATCH 3/3] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- pyproject.toml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 2b72c35..7b35b76 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -108,10 +108,10 @@ qt = "*" qtpy = "*" pyqt = "*" # pip-audit -h2 = ">=4.3.0" # Known vulnerability in <4.3.0 +h2 = ">=4.3.0" # Known vulnerability in <4.3.0 brotli = ">=1.2.0" -urllib3 = ">=2.6.3" # Known vulnerability in <2.6.3 -filelock = ">=3.20.3" # Known vulnerability in <3.20.3 +urllib3 = ">=2.6.3" # Known vulnerability in <2.6.3 +filelock = ">=3.20.3" # Known vulnerability in <3.20.3 virtualenv = ">=20.36.1" # Known vulnerability in <20.36.1 [tool.pixi.pypi-dependencies]